Hello Hai,
Thank you for your reply.
Without the nofit keyword, I obtain the following values:
1 0.0315
2 0.0574
3 0.0775
4 0.0939
5 0.1062
*ZIADA Sonia*
PhD Student, Structural Bioinformatics & Chemoinformatics
Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université
d'Orléans 7311
Rue de Chartres, 45067 Orléans, France
T. +33 238 419 939
2017-10-04 1:22 GMT+02:00 Hai Nguyen <nhai.qn.gmail.com>:
> Can you rerun without the nofit keyword?
>
> Hai
>
> On Tue, Oct 3, 2017 at 5:05 PM Sonia Ziada <sonia.ziada.gmail.com> wrote:
>
> > Dear Carlos,
> >
> > Thank you for your reply.
> >
> > - I am writing the trajectory (netcdf file) and the mdout every 2 steps
> > (ntwx=2 and ntpr=2), so the structures used in cpptraj should correspond
> > exactly to those in the MD run.
> > - I am sure that the reference used for the fitting in the MD run is the
> > same that those I use in cpptraj
> > - I have also checked that the masks are correct (by looking at: the
> header
> > of the mdout, the output of cpptraj and by using ambmask program)
> > - Finally, I have a looked at the ene.F90 sander script containing the
> > subroutine fitrms (that calcutes the current rmsd after the fitting step)
> > to ensure that the rmsd is mass weighted.
> >
> > I do not understand the difference in rmsd values between cpptraj and the
> > mdout file. By calcutating the rmsd with cpptraj, I assumed that the
> > alignment algorithm is the same in cpptraj as in sander. But is this
> true?
> >
> >
> > *ZIADA Sonia*
> > PhD Student, Structural Bioinformatics & Chemoinformatics
> > Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université
> > d'Orléans 7311
> > Rue de Chartres, 45067 Orléans, France
> > T. +33 238 419 939
> >
> > 2017-10-03 18:44 GMT+02:00 Carlos Simmerling <
> carlos.simmerling.gmail.com
> > >:
> >
> > > are you certain that the structures that you are using in ptraj
> > correspond
> > > exactly to those in the MD run? for example, are you writing every
> step?
> > > and are you using netcdf format instead of the low precision trajectory
> > > files?
> > >
> > > On Tue, Oct 3, 2017 at 7:36 AM, Sonia Ziada <sonia.ziada.gmail.com>
> > wrote:
> > >
> > > > Dear Amber users,
> > > >
> > > > I am having trouble understanding how the RMSD is calculated in
> > targeted
> > > MD
> > > > simulations.
> > > >
> > > > I am using tgtfitmask (:Mask1) and tgtrmsmask (:Mask2).
> > > > I try to reproduce the sander output's targeted rmsd results (those
> > > > available in the mdout file: “current rmsd from reference”) using
> > cpptraj
> > > > with the following commands:
> > > >
> > > > ### cpptraj script ---------------------------------
> > > > parm topo.top
> > > > trajin traj.nc
> > > > reference reference.rst
> > > > rms reference :Mask1
> > > > rms reference mass :Mask2 out rmsd.dat nofit
> > > > run
> > > > quit
> > > > --------------------------------------------------------
> > > >
> > > >
> > > > *But I get different results: *
> > > > ### 1) From the .mdout file:
> > > > Current RMSD from reference: 0.017
> > > > Current RMSD from reference: 0.049
> > > > Current RMSD from reference: 0.075
> > > > Current RMSD from reference: 0.094
> > > > Current RMSD from reference: 0.110
> > > >
> > > > ### 2) From cpptraj (rmsd.dat file)
> > > > 1 0.0337
> > > > 2 0.0630
> > > > 3 0.0853
> > > > 4 0.1027
> > > > 5 0.1178
> > > >
> > > > As far as I can conclude with these results, the TMD's alignment
> sceme
> > > > seems different from cpptraj's alignment sceme. How can I reproduce
> the
> > > > rmsd of the mdout using cpptraj ?
> > > > Thank you.
> > > >
> > > >
> > > > *ZIADA Sonia*
> > > > PhD Student, Structural Bioinformatics & Chemoinformatics
> > > > Institut de Chimie Organique et Analytique (ICOA), UMR
> CNRS-Université
> > > > d'Orléans 7311
> > > > Rue de Chartres, 45067 Orléans, France
> > > > T. +33 238 419 939
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Received on Wed Oct 04 2017 - 00:30:02 PDT
